Nahomi Kawasumi put the Japanese team ahead in the 33rd minute and Aya Miyama doubled the lead in the 44th at the City of Coventry Stadium.
Melissa Tancredi pulled one back from close range for Canada in the 55th, taking Rhian Wilkinson's low cross from the right wing and skipping in front of defender Yukari Kinga to score.
Japan, which upset the United States to win the Women's World Cup last year, started strong against the Canadians and only allowed a few opportunities in the first half.
But Canada made it more difficult in the second half with some composed play that led to Tancredi's goal.
Japan missed an early chance when Kinga floated a ball into the box and Homare Sawa volleyed over the bar in the fifth minute.
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